RE: AMBER: xleap with modified residue

From: Ross Walker <>
Date: Thu, 20 Oct 2005 11:58:53 -0700

Dear Whitney,
This sounds like it could be a bug with leap. Can you try repeating all the
steps but this time call the unit MGG instead of 2MG. The number at the
beginning of the unit name may be giving problems. Also replace the unit
name mol with test. So
test = loadpdb test.pdb
Please make sure you have applied all the bugfixes from first since several of these deal
with leap crashes.
If you still have problems please email me back with the library and pdb
files and I'll see if I can reproduce the error.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
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From: [] On Behalf Of
Whitney Allen
Sent: Thursday, October 20, 2005 11:13
Subject: AMBER: xleap with modified residue

Hi Amber users

I am trying to run MD on a TRNA structure (6tna.pdb). This molecule has
several modified bases and so I have used Antechamber to compute a molecule
library for each modified base. However, after loading the library file
into xleap (which is successful) I try and load the TRNA structure and xleap
completely shuts down.

Below is the procedure that I follow. Note that I have tried to follow
tutorials 4 & 5 as applicable. Here, for simplicity, I have cut the TRNA
PDB file so that it contains only one modified residue (2MG or residue 10 in
the 6tna.pdb file) and 15 total residues (residues 1-15 in the 6tna.pdb
file) and have called it test.pdb. If anyone can help please reply and I can
send you the 2MG.pdb, 2MG.mol2, 2mg.lib, and test.pdb files.


(Antechamber- note that I change the residue to a molecule)


% $AMBERHOME/exe/antechamber -i 2MG.pdb -fi pdb -o 2MG.mol2 -fo mol2 -c bcc


% $AMBERHOME/exe/parmchk -i 2MG.mol2 -f mol2 -o 2MG.frcmod


% xleap -f leaprc.rna.ff99

source leaprc.gaff

loadmol2 2MG.mol2

check 2MG

edit 2MG

loadamberparms 2MG.frcmod

check 2MG

saveoff 2MG.lib

desc 2MG



% xleap -f leaprc.rna.ff99

source leaprc.gaff

loadoff 2mg.lib

check 2MG

mol=loadpdb test.pdb


(At this point xleap closes and I get the following error)


!FATAL ERROR----------------------------------------

!FATAL: In file [chirality.c], line 120

!FATAL: Message: Atom P is not in the first list




Please help me understand what is going on here and let me know how I can
get this to work. It looks like all of the files are of normal format so I
am a bit confused.

Thanks in advance

Whitney Hastings


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Received on Thu Oct 20 2005 - 20:53:00 PDT
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